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- PDB-8fg5: Apo mouse acidic mammalian chitinase, catalytic domain at 100 K -

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Basic information

Entry
Database: PDB / ID: 8fg5
TitleApo mouse acidic mammalian chitinase, catalytic domain at 100 K
ComponentsAcidic mammalian chitinase
KeywordsHYDROLASE / GH18 chitinase / acidic mammalian chitinase
Function / homology
Function and homology information


Digestion of dietary carbohydrate / production of molecular mediator involved in inflammatory response / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / immune system process / polysaccharide catabolic process / positive regulation of chemokine production ...Digestion of dietary carbohydrate / production of molecular mediator involved in inflammatory response / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / immune system process / polysaccharide catabolic process / positive regulation of chemokine production / apoptotic process / extracellular space / cytoplasm
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Acidic mammalian chitinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDiaz, R.E. / Correy, G.J. / Young, I.D. / Thompson, M.C. / Fraser, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Other governmentT29IP0554 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM124169 United States
CitationJournal: Biorxiv / Year: 2024
Title: Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase.
Authors: Diaz, R.E. / Ecker, A.K. / Correy, G.J. / Asthana, P. / Young, I.D. / Faust, B. / Thompson, M.C. / Seiple, I.B. / Van Dyken, S.J. / Locksley, R.M. / Fraser, J.S.
History
DepositionDec 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 10, 2024Group: Database references / Category: citation / Item: _citation.year
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6462
Polymers44,6221
Non-polymers241
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.040, 42.250, 67.410
Angle α, β, γ (deg.)90.000, 95.180, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Acidic mammalian chitinase / AMCase / YNL


Mass: 44621.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Chia, Chia1 / Plasmid: mAMCase_CatD_6xHis_pTwistCMV / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q91XA9, chitinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 11 mg/mL AMCase catalytic domain 20% w/v PEG 6000 0.1 M Sodium Acetate pH 5.0 0.2 M Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11664 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11664 Å / Relative weight: 1
ReflectionResolution: 1.3→59.79 Å / Num. obs: 83050 / % possible obs: 99.96 % / Redundancy: 25.3 % / Biso Wilson estimate: 15.81 Å2 / CC1/2: 0.976 / CC star: 0.98 / Rmerge(I) obs: 0.1342 / Rpim(I) all: 0.02718 / Rrim(I) all: 0.137 / Net I/σ(I): 13.31
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.3-1.3222.72.3291.741290.8220.4932.382
3.53-59.8624.40.08342.243110.9990.0170.084

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia20.3.8.0data reduction
DIALS2.2.10-g6dafd9427-releasedata scaling
PHASER2.8.3phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fxy

3fxy


Resolution: 1.3→59.79 Å / SU ML: 0.1264 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.4657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1518 4099 4.94 %
Rwork0.1317 78948 -
obs0.1327 83047 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.71 Å2
Refinement stepCycle: LAST / Resolution: 1.3→59.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 1 474 3482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00593214
X-RAY DIFFRACTIONf_angle_d0.87464391
X-RAY DIFFRACTIONf_chiral_restr0.0751447
X-RAY DIFFRACTIONf_plane_restr0.0079577
X-RAY DIFFRACTIONf_dihedral_angle_d11.58831142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.30351400.27292688X-RAY DIFFRACTION99.96
1.32-1.330.24261600.2292711X-RAY DIFFRACTION99.97
1.33-1.350.2381390.20582700X-RAY DIFFRACTION100
1.35-1.370.2461470.19222712X-RAY DIFFRACTION99.97
1.37-1.380.20221490.18192691X-RAY DIFFRACTION99.96
1.38-1.40.25351240.17982719X-RAY DIFFRACTION100
1.4-1.430.20091440.1682678X-RAY DIFFRACTION100
1.43-1.450.21061210.16312723X-RAY DIFFRACTION100
1.45-1.470.1841440.14712727X-RAY DIFFRACTION100
1.47-1.50.2051510.14042698X-RAY DIFFRACTION100
1.5-1.520.15561390.13232713X-RAY DIFFRACTION100
1.52-1.550.14731330.1252688X-RAY DIFFRACTION100
1.55-1.590.16071410.11922710X-RAY DIFFRACTION100
1.59-1.620.14351560.11582723X-RAY DIFFRACTION100
1.62-1.660.15881500.11772702X-RAY DIFFRACTION100
1.66-1.70.16321350.11722711X-RAY DIFFRACTION100
1.7-1.740.1441360.11432719X-RAY DIFFRACTION100
1.74-1.80.15931670.11852679X-RAY DIFFRACTION100
1.8-1.850.13781280.11912733X-RAY DIFFRACTION100
1.85-1.920.14071340.1242742X-RAY DIFFRACTION100
1.92-20.15741350.12632729X-RAY DIFFRACTION100
2-2.090.15921500.1212706X-RAY DIFFRACTION100
2.09-2.20.14791440.11532730X-RAY DIFFRACTION100
2.2-2.340.12911360.11792739X-RAY DIFFRACTION99.97
2.34-2.520.14091260.12342766X-RAY DIFFRACTION100
2.52-2.770.16051350.13192743X-RAY DIFFRACTION100
2.77-3.170.15841450.13722754X-RAY DIFFRACTION100
3.17-3.990.11731470.12422765X-RAY DIFFRACTION100
4-59.790.14451430.13652849X-RAY DIFFRACTION99.97

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